Sea-level rise (SLR) is a projected consequence of global climate change that will result in complex changes in coastal ecosystems. These changes will cause transitions among coastal habitat types, which will be compounded by human-made barriers to the gradual inland migration of these habitat types. The effect of these changes on the future viability of coastal species will depend on the habitat requirements and population dynamics of these species. Thus, realistic assessments of the impact of SLR require linking geomorphological models with habitat and population models. In this study, we implemented a framework that allows this linkage, and demonstrated its feasibility to assess the effect of SLR on the viability of the Snowy Plover population in Florida. The results indicate that SLR will cause a decline in suitable habitat and carrying capacity for this species, and an increase in the risk of its extinction and decline. The model projected that the population size will decline faster than the area of habitat or carrying capacity, demonstrating the necessity of incorporating population dynamics in assessing the impacts of SLR on coastal species. The results were most sensitive to uncertainties in survival rate and fecundity, and suggested that future studies on this species should focus on the average and variability of these demographic rates and their dependence on population density. The effect of SLR on this species’ viability was qualitatively similar with most alternative models that used the extreme values of each uncertain parameter, indicating that the results are robust to uncertainties in the model.